Contacts of the helix formed by residues 1011 - 1026 (chain W) in PDB entry 5O9G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1011 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009W SER 4.1 1.8 + - - -
1010W ILE* 1.3 72.7 - - - +
1012W GLU* 1.3 63.5 + - - -
1014W GLU* 3.3 20.8 + - - -
1015W VAL* 3.1 32.6 + - - +
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Residues in contact with GLU1012 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011W GLY* 1.3 71.2 - - - -
1013W SER* 1.3 60.7 + - - +
1015W VAL* 3.2 5.7 + - - +
1016W ARG* 2.9 56.0 + - - +
1123W LYS* 2.9 30.0 - - - +
1124W GLY* 3.9 5.9 - - - -
1125W VAL* 3.3 18.2 + - - +
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Residues in contact with SER1013 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-70J C 4.0 12.4 + - - -
1012W GLU* 1.3 79.1 - - - +
1014W GLU* 1.3 76.6 + - - +
1016W ARG* 3.5 17.2 - - - +
1017W ALA* 2.9 31.7 + - - +
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Residues in contact with GLU1014 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009W SER 5.3 1.8 - - - +
1010W ILE* 3.6 31.2 - - + -
1011W GLY* 3.3 23.7 + - - +
1012W GLU 3.1 0.4 - - - -
1013W SER* 1.3 90.2 + - - +
1015W VAL* 1.3 60.8 + - - +
1017W ALA* 4.5 3.6 - - - -
1018W LEU* 2.9 32.7 + - - +
1041W LEU* 4.9 2.9 - - + +
1042W PRO* 3.4 39.6 - - + +
1044W LYS* 5.1 6.2 + - + +
1049W TYR* 5.5 4.4 - - + +
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Residues in contact with VAL1015 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010W ILE* 3.6 18.4 - - + +
1011W GLY 3.1 17.7 + - - +
1012W GLU* 3.2 6.7 + - - +
1014W GLU* 1.3 76.4 - - - +
1016W ARG* 1.3 58.1 + - - +
1018W LEU* 3.8 6.3 - - + +
1019W TYR* 2.9 27.7 + - - +
1052W THR* 6.4 0.4 - - + -
1056W MET* 4.5 13.0 - - + +
1122W PHE* 4.2 26.7 - - + +
1123W LYS* 5.0 13.5 - - + +
1125W VAL* 3.6 27.8 - - + -
1128W LEU* 5.1 3.8 - - + -
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Residues in contact with ARG1016 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-71J T 3.5 46.8 + - - -
-70J C 2.7 43.3 + - - +
1012W GLU* 2.9 40.8 + - - +
1013W SER* 3.5 22.6 - - - +
1015W VAL* 1.3 74.2 - - - +
1017W ALA* 1.3 59.2 + - - +
1019W TYR* 3.2 7.5 + - - +
1020W LYS* 2.9 44.9 + - - +
1125W VAL* 3.8 26.2 - - + +
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Residues in contact with ALA1017 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-70J C 4.7 5.3 + - - +
1013W SER 2.9 22.1 + - - +
1014W GLU* 4.3 4.0 - - - +
1016W ARG* 1.3 76.3 - - - +
1018W LEU* 1.3 57.8 + - - +
1020W LYS* 3.4 10.8 + - - +
1021W ALA* 2.9 26.9 + - - +
1040W THR* 3.8 33.9 - - + +
1041W LEU* 4.6 4.5 - - + -
1042W PRO* 6.3 0.4 - - + -
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Residues in contact with LEU1018 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010W ILE* 5.9 4.9 - - + -
1014W GLU 2.9 22.1 + - - +
1015W VAL* 3.9 5.4 - - - +
1017W ALA* 1.3 73.4 - - - +
1019W TYR* 1.3 59.7 + - - +
1021W ALA* 3.1 5.6 + - + +
1022W ILE* 2.9 40.5 + - + +
1028W LEU* 3.6 31.2 - - + -
1041W LEU* 3.9 25.9 - - + +
1049W TYR* 4.0 24.2 - - + +
1052W THR* 3.7 26.5 - - - +
1053W TYR* 5.1 5.4 - - + +
1056W MET* 5.1 11.7 - - + -
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Residues in contact with TYR1019 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I A 5.9 4.3 - - - -
1015W VAL* 2.9 20.3 + - + +
1016W ARG* 3.5 9.0 - - - +
1018W LEU* 1.3 77.0 - - - +
1020W LYS* 1.3 60.2 + - + +
1022W ILE* 3.1 9.7 + - - +
1023W LEU* 2.9 57.0 + - + +
1056W MET* 3.8 22.8 - - + +
1120W PHE* 5.6 0.4 - + - -
1127W SER 5.1 1.8 - - - -
1128W LEU* 3.7 39.7 - - + -
1129W ASN* 2.9 36.1 + - - +
1132W SER* 5.3 1.4 - - - -
1133W LEU* 3.6 32.7 - - + +
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Residues in contact with LYS1020 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I T 6.4 2.2 - - - -
-71J T 4.2 17.8 + - - -
-70J C 4.4 17.9 + - - -
1016W ARG* 2.9 39.5 + - - +
1017W ALA* 3.7 7.9 - - - +
1019W TYR* 1.3 75.7 - - + +
1021W ALA* 1.3 60.8 + - - +
1023W LEU* 3.1 15.8 + - + +
1024W LYS* 2.9 35.6 + - - +
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Residues in contact with ALA1021 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017W ALA 2.9 15.1 + - - +
1018W LEU* 3.1 15.7 + - + +
1020W LYS* 1.3 76.0 - - - +
1022W ILE* 1.3 58.9 + - - +
1024W LYS* 4.5 4.9 - - - +
1025W PHE* 2.9 40.1 + - + +
1026W GLY 3.6 1.0 + - - +
1028W LEU* 4.3 15.1 - - + +
1035W LEU* 5.3 6.3 - - + +
1040W THR* 5.7 3.8 - - + -
1041W LEU* 5.0 10.5 - - + -
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Residues in contact with ILE1022 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018W LEU* 2.9 24.4 + - + +
1019W TYR* 3.1 8.3 + - - +
1021W ALA* 1.3 75.0 - - - +
1023W LEU* 1.3 61.1 + - - +
1024W LYS 3.1 0.4 - - - -
1026W GLY* 2.9 37.3 + - - +
1028W LEU* 3.8 17.0 - - + -
1053W TYR* 3.6 31.2 - - + +
1056W MET* 3.7 31.9 - - + -
1057W MET* 5.1 6.1 - - - -
1133W LEU* 3.7 28.0 - - + +
1136W ARG* 3.8 7.9 - - + +
1137W VAL* 5.3 4.0 - - + -
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Residues in contact with LEU1023 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I A 3.8 28.3 - - - +
1019W TYR* 2.9 44.8 + - + +
1020W LYS* 3.1 15.7 + - + +
1022W ILE* 1.3 76.7 - - - +
1024W LYS* 1.3 57.6 + - - +
1132W SER* 4.7 16.6 - - - +
1133W LEU* 3.8 24.5 - - + -
1136W ARG* 2.4 46.3 + - + +
1192W TYR* 4.0 7.5 - - - +
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Residues in contact with LYS1024 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020W LYS* 2.9 19.1 + - - +
1021W ALA* 4.6 0.9 - - - -
1023W LEU* 1.3 79.4 - - - +
1025W PHE* 1.3 88.3 + - + +
1140W LEU* 4.2 7.6 - - - +
1190W TYR 4.0 5.4 - - - +
1191W GLY* 3.5 20.4 - - - -
1192W TYR 3.6 19.9 + - - +
1193W GLY* 3.9 5.7 + - - -
1194W SER* 2.6 37.8 + - - +
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Residues in contact with PHE1025 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021W ALA* 2.9 19.2 + - + +
1024W LYS* 1.3 104.4 - - + +
1026W GLY* 1.3 65.2 + - - +
1027W ASN 3.4 9.1 + - - +
1031W ILE* 4.5 16.0 - - + +
1035W LEU* 3.6 46.4 - - + -
1038W ASP* 5.6 4.5 - - - -
1140W LEU* 3.5 16.5 - - - +
1144W LYS* 6.0 2.6 - - - -
1189W LYS 4.8 7.4 - - - -
1190W TYR* 3.7 23.6 - - - -
1191W GLY* 5.6 0.4 - - - -
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Residues in contact with GLY1026 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021W ALA 3.6 1.6 + - - +
1022W ILE* 2.9 38.0 + - - +
1025W PHE* 1.3 73.1 - - - +
1027W ASN* 1.3 65.4 + - - -
1028W LEU* 3.4 7.4 + - - +
1053W TYR* 3.9 13.4 - - - -
1136W ARG* 4.8 1.8 - - - -
1137W VAL* 4.7 10.1 - - - -
1140W LEU* 3.6 13.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il